Chapter 5 Alpha diversity

5.1 Filtered

#Calculate Hill numbers
richness <- genome_counts_filt %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=0) %>%
            t() %>%
            as.data.frame() %>%
            rename(richness=1) %>%
            rownames_to_column(var="microsample")

neutral <- genome_counts_filt %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=1) %>%
            t() %>%
            as.data.frame() %>%
            rename(neutral=1) %>%
            rownames_to_column(var="microsample")

phylogenetic <- genome_counts_filt %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=1,tree=genome_tree) %>%
            t() %>%
            as.data.frame() %>%
            rename(phylogenetic=1) %>%
            rownames_to_column(var="microsample")

# Merge alpha diversities
alpha_diversity <- richness %>%
      full_join(neutral,by=join_by(microsample==microsample)) %>%
      full_join(phylogenetic,by=join_by(microsample==microsample)) %>%
      left_join(sample_metadata, by=join_by(microsample==microsample))

# Write alpha diversities
alpha_diversity %>% write_tsv("results/alpha_div_filtered.tsv")

# Print alpha diversity
alpha_diversity %>%
  select(microsample,richness, neutral, phylogenetic, section, buffer, batch, Xcoord, Ycoord, size) %>%
  tt()
tinytable_8x9sj8eztwd1brqj29x0
microsample richness neutral phylogenetic section buffer batch Xcoord Ycoord size
M300554 105 45.801912 3.937760 Caecum right B11 MSEB0006 74953.33 27445.67 4976
M300555 3 2.654441 1.663073 Caecum right B11 MSEB0006 72020.28 33695.14 4976
M300556 3 2.921247 1.820079 Caecum right B11 MSEB0006 75415.39 27819.35 4976
M300557 81 43.169579 3.736918 Caecum right B11 MSEB0006 76113.48 28351.85 4976
M300559 105 46.235275 3.950650 Caecum right B11 MSEB0006 76849.23 29025.05 4976
M300560 99 44.437305 4.093363 Caecum right B11 MSEB0006 75971.70 29352.86 4976
M300561 103 44.311493 4.120349 Caecum right B11 MSEB0006 76680.94 29558.16 4976
M300562 103 46.882732 4.048584 Caecum right B11 MSEB0006 74883.32 29170.18 5140
M300563 109 47.059960 4.017112 Caecum right B11 MSEB0006 75220.99 29120.51 5140
M300564 12 10.477468 2.973998 Caecum right B11 MSEB0006 75894.62 29134.86 5140
M300566 93 43.059847 3.786416 Caecum right B11 MSEB0006 76922.54 29224.45 5140
M300567 99 44.029116 4.039769 Caecum right B11 MSEB0006 77492.20 29097.78 5140
M300569 100 46.805777 4.129635 Caecum right B11 MSEB0006 77495.46 28977.76 5140
M300570 100 44.462204 3.978752 Caecum right B11 MSEB0006 74950.84 28473.11 4815
M300571 94 42.482781 3.903377 Caecum right B11 MSEB0006 75619.95 28632.40 4815
M300572 56 32.680577 3.764339 Caecum right B11 MSEB0006 76345.93 29031.81 4815
M300574 97 43.914978 3.991990 Caecum right B11 MSEB0006 76921.00 29347.99 4815
M300576 92 43.158898 3.979982 Caecum right B11 MSEB0006 77104.53 29588.79 4815
M300577 103 44.666492 4.003275 Caecum right B11 MSEB0006 77418.90 29907.92 4815
M300578 101 44.526067 3.942073 Caecum right B12 MSEB0006 76897.21 30198.48 5140
M300580 102 43.777961 3.966526 Caecum right B12 MSEB0006 77026.94 30039.53 5140
M300581 79 39.975639 3.898216 Caecum right B12 MSEB0006 77028.60 29718.20 5140
M300582 78 38.898531 3.907879 Caecum right B12 MSEB0006 77019.21 29448.24 5140
M300583 95 38.373844 4.002493 Caecum right B12 MSEB0006 77009.20 28923.10 5140
M300584 104 44.918626 3.992409 Caecum right B12 MSEB0006 77019.41 28061.84 5140
M300588 102 42.618728 3.997889 Caecum right B12 MSEB0006 75330.02 26890.36 5141
M300589 99 41.459691 3.963052 Caecum right B12 MSEB0006 75862.87 27323.96 5141
M300590 96 40.482162 4.131238 Caecum right B12 MSEB0006 76508.23 27653.84 5141
M300592 103 40.971234 4.092363 Caecum right B12 MSEB0006 77351.46 28017.27 5141
M300593 98 42.126550 4.082443 Caecum right B12 MSEB0006 77854.22 28261.49 5141
M300594 96 43.659879 4.066965 Caecum right B12 MSEB0006 75509.65 26477.82 4976
M300595 102 37.738766 4.076473 Caecum right B12 MSEB0006 75650.54 26591.91 4976
M300596 105 40.160724 4.060594 Caecum right B12 MSEB0006 75822.84 26598.11 4976
M300597 100 40.582505 4.107775 Caecum right B12 MSEB0006 76147.10 26625.28 4976
M300598 101 41.887011 4.052863 Caecum right B12 MSEB0006 76899.24 26623.52 4976
M300599 104 42.932100 3.970582 Caecum right B12 MSEB0006 76852.73 26643.02 4976
M300602 4 3.258694 1.449831 Ileum B11 MSEB0006 104424.70 42749.48 5140
M300603 3 2.026603 1.266765 Ileum B11 MSEB0006 104606.90 42459.54 5140
M300605 2 1.729081 1.216363 Ileum B11 MSEB0006 104954.50 42730.89 5140
M300606 1 1.000000 1.000000 Ileum B11 MSEB0006 105122.50 42666.74 5140
M300608 4 2.614424 1.430317 Ileum B11 MSEB0006 105262.70 42589.77 5140
M300609 4 3.096111 1.458992 Ileum B11 MSEB0006 105328.90 42703.60 5140
M300610 4 3.092445 1.481998 Ileum B11 MSEB0006 105102.40 41497.10 4976
M300611 1 1.000000 1.000000 Ileum B11 MSEB0006 105146.00 41596.22 4976
M300612 4 3.200070 1.470375 Ileum B11 MSEB0006 105281.00 41702.52 4976
M300613 1 1.000000 1.000000 Ileum B11 MSEB0006 105408.30 41533.66 4976
M300616 3 1.602470 1.194510 Ileum B11 MSEB0006 105595.70 41999.37 4976
M300617 4 2.597621 1.413674 Ileum B11 MSEB0006 105983.00 42106.21 4976
M300619 3 1.859573 1.239761 Ileum B11 MSEB0006 106845.70 41525.80 5306
M300622 3 2.658765 1.355956 Ileum B11 MSEB0006 107262.30 42133.87 5306
M300623 3 2.873136 1.383011 Ileum B11 MSEB0006 107820.60 41925.02 5306
M300624 1 1.000000 1.000000 Ileum B11 MSEB0006 107233.50 41764.35 5306
M300627 3 2.862931 1.381746 Ileum B12 MSEB0006 108112.00 45420.81 4815
M300628 4 2.628829 1.503377 Ileum B12 MSEB0006 108221.60 45346.45 4815
M300629 4 1.907144 1.304654 Ileum B12 MSEB0006 108085.50 45636.13 4815
M300630 4 1.854313 1.283251 Ileum B12 MSEB0006 108093.70 45848.93 4815
M300631 5 3.608828 1.726759 Ileum B12 MSEB0006 107697.50 45704.29 4815
M300633 6 2.179216 1.436402 Ileum B12 MSEB0006 107727.50 45487.09 4815
M300634 5 2.654260 1.436436 Ileum B12 MSEB0006 106635.90 42106.55 5384
M300636 4 2.513021 1.488272 Ileum B12 MSEB0006 106545.50 42220.70 5384
M300638 4 2.712719 1.467680 Ileum B12 MSEB0006 106647.00 42288.86 5384
M300639 7 2.562594 1.490282 Ileum B12 MSEB0006 106800.50 41821.88 5384
M300640 3 2.025162 1.266492 Ileum B12 MSEB0006 107052.70 42525.49 5384
M300642 1 1.000000 1.000000 Ileum B12 MSEB0006 108030.70 43599.50 4976
M300644 5 1.600004 1.210094 Ileum B12 MSEB0006 NA NA NA
M300645 5 1.502894 1.241772 Ileum B12 MSEB0006 107988.20 43509.47 4976
M300647 5 3.154388 1.460507 Ileum B12 MSEB0006 107969.50 43138.84 4976
M300648 5 1.758864 1.268011 Ileum B12 MSEB0006 107883.70 43169.50 4976
M300704 47 26.137840 3.656487 Colon B11 MSEB0010 10676.97 15665.82 5140
M300705 62 39.308166 3.660768 Colon B11 MSEB0010 10812.32 15756.81 5140
M300706 58 33.851408 3.774257 Colon B11 MSEB0010 11055.42 15656.04 5140
M300707 74 38.632295 3.920088 Colon B11 MSEB0010 11216.84 15649.19 5140
M300708 85 41.477440 3.830608 Colon B11 MSEB0010 11879.87 15812.03 5140
M300711 83 40.402932 3.871549 Colon B11 MSEB0010 12278.13 15716.47 5140
M300712 84 42.428071 3.859852 Colon B11 MSEB0010 12139.94 15889.85 4976
M300714 77 39.203234 3.974200 Colon B11 MSEB0010 12138.96 16135.22 4976
M300715 84 41.934901 3.820654 Colon B11 MSEB0010 12164.85 16944.14 4976
M300716 64 38.066001 3.624855 Colon B11 MSEB0010 12650.44 17948.63 4976
M300717 66 38.461828 3.862272 Colon B11 MSEB0010 13434.73 19286.92 4976
M300718 96 46.399944 3.883736 Colon B11 MSEB0010 13238.20 20246.16 4976
M300721 92 47.317073 3.759318 Colon B11 MSEB0010 10372.82 20398.48 5306
M300722 56 33.260330 3.727113 Colon B11 MSEB0010 11173.11 20408.59 5306
M300724 80 43.719402 3.794995 Colon B11 MSEB0010 13295.25 18310.97 5306
M300725 21 17.447617 2.930725 Colon B11 MSEB0010 12939.03 18128.54 5306
M300727 81 41.998480 3.947856 Colon B11 MSEB0010 12777.09 17606.38 5306
M300729 8 7.637585 2.619316 Colon B11 MSEB0010 12551.79 21653.42 4815
M300730 14 12.494169 2.806653 Colon B11 MSEB0010 12478.73 21318.48 4815
M300731 78 42.804279 3.541318 Colon B11 MSEB0010 12362.88 20562.75 4815
M300733 29 21.650469 3.174838 Colon B11 MSEB0010 12653.67 19720.44 4815
M300735 67 39.697104 3.650732 Colon B11 MSEB0010 11471.31 19136.40 4815
M300736 89 44.552604 3.826006 Colon B11 MSEB0010 13507.34 18129.93 5647
M300738 85 45.260227 3.746172 Colon B11 MSEB0010 13010.06 17942.33 5647
M300741 75 40.579742 3.741690 Colon B11 MSEB0010 12684.37 17716.75 5647
M300742 82 42.384536 3.881068 Colon B11 MSEB0010 12621.55 17543.54 5647
M300743 76 41.817272 3.730852 Colon B11 MSEB0010 12372.90 16657.60 5647
M300744 32 24.141380 3.136654 Colon B11 MSEB0010 11994.45 14153.13 4976
M300745 59 36.354256 3.462527 Colon B11 MSEB0010 12007.50 14299.24 4976
M300747 85 45.968277 3.649012 Colon B11 MSEB0010 12029.35 14662.48 4976
M300748 64 37.120180 3.504468 Colon B11 MSEB0010 12076.59 15671.87 4976
M300750 73 39.843866 3.738390 Colon B11 MSEB0010 12060.51 16688.98 4976
M300751 80 43.869573 3.738696 Colon B11 MSEB0010 11931.20 19713.77 4976
M300753 65 35.118403 3.589983 Colon B12 MSEB0010 13884.30 20066.13 4815
M300755 76 38.643425 3.896215 Colon B12 MSEB0010 13715.68 19528.97 4815
M300756 103 43.201393 3.990432 Colon B12 MSEB0010 13508.64 19087.25 4815
M300757 83 39.509499 3.977505 Colon B12 MSEB0010 13209.32 18911.46 4815
M300758 98 47.502632 3.784666 Colon B12 MSEB0010 13454.50 18211.88 4815
M300759 105 45.507585 4.065463 Colon B12 MSEB0010 13356.63 17525.29 4815
M300760 78 37.482344 3.895542 Colon B12 MSEB0010 12866.49 15050.07 5140
M300761 115 45.578238 4.024987 Colon B12 MSEB0010 12921.94 15311.99 5140
M300763 125 50.960537 3.971121 Colon B12 MSEB0010 12995.95 15577.55 5140
M300764 115 48.329755 3.842227 Colon B12 MSEB0010 12999.11 16205.10 5140
M300766 112 46.704807 4.063781 Colon B12 MSEB0010 13128.60 18741.54 5140
M300767 100 41.243887 3.894222 Colon B12 MSEB0010 13103.68 20085.08 5140
M300768 79 38.784598 3.840394 Colon B12 MSEB0010 12299.78 15261.25 4815
M300771 58 34.643272 3.720942 Colon B12 MSEB0010 12230.64 14216.24 4815
M300772 102 47.639783 3.790707 Colon B12 MSEB0010 12192.80 14393.52 4815
M300773 106 50.262746 3.545739 Colon B12 MSEB0010 12122.68 16011.33 4815
M300774 114 46.306826 4.058256 Colon B12 MSEB0010 12155.62 16716.47 4815
M300775 92 40.482612 3.917541 Colon B12 MSEB0010 12941.43 17792.21 4815
M300776 71 37.655019 3.747935 Colon B12 MSEB0010 10481.87 16446.70 5306
M300778 82 41.038918 3.831210 Colon B12 MSEB0010 10349.88 16974.87 5306
M300780 88 40.130094 3.880301 Colon B12 MSEB0010 10386.11 17635.79 5306
M300782 86 39.302414 3.892170 Colon B12 MSEB0010 10499.61 18348.85 5306
M300783 67 37.371632 3.772192 Colon B12 MSEB0010 10505.18 19231.33 5306
M300784 63 33.764525 3.734824 Colon B12 MSEB0010 11637.20 19482.30 4656
M300786 44 28.493828 3.612460 Colon B12 MSEB0010 11099.18 18995.87 4656
M300787 106 45.535131 3.977904 Colon B12 MSEB0010 10460.97 19686.94 4656
M300788 62 33.583894 3.720720 Colon B12 MSEB0010 10442.08 20914.36 4656
M300791 47 26.239698 3.687149 Colon B12 MSEB0010 11146.56 21763.22 4656
M300792 103 44.068606 4.152050 Colon B12 MSEB0010 11630.33 20543.59 5140
M300794 105 44.712540 3.957158 Colon B12 MSEB0010 11673.94 21223.36 5140
M300797 96 39.849925 3.926466 Colon B12 MSEB0010 12879.98 20904.88 5140
M300798 116 39.422201 4.074559 Colon B12 MSEB0010 12256.49 21371.45 5140 
# Print alpha diversity summary
alpha_diversity %>%
  select(richness, neutral, phylogenetic, section, batch) %>%
  group_by(section, batch) %>%
  summarise(richness=mean(richness), neutral=mean(neutral), phylogenetic=mean(phylogenetic)) %>%
  tt()
tinytable_qfacpcfg64x0i8t7yu7n
section batch richness neutral phylogenetic
Caecum right MSEB0006 89.50000 39.563947 3.840313
Colon MSEB0010 77.96923 38.850665 3.748993
Ileum MSEB0006 3.59375 2.222942 1.322728 
alpha_diversity %>%
  pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
  left_join(quality,by=join_by(microsample==microsample)) %>%
  mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
  ggplot(aes(x=section, y=value, color=quality, group=section))+ 
        scale_color_gradient(low = "red", high = "green", name = "Quality") +
        geom_boxplot(outlier.shape = NA) +
        geom_jitter(width=0.2) + 
        facet_grid(metric ~ section, scales = "free")

5.2 Unfiltered

#Calculate Hill numbers
richness <- genome_counts %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=0) %>%
            t() %>%
            as.data.frame() %>%
            rename(richness=1) %>%
            rownames_to_column(var="microsample")

neutral <- genome_counts %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=1) %>%
            t() %>%
            as.data.frame() %>%
            rename(neutral=1) %>%
            rownames_to_column(var="microsample")

phylogenetic <- genome_counts %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=1,tree=genome_tree) %>%
            t() %>%
            as.data.frame() %>%
            rename(phylogenetic=1) %>%
            rownames_to_column(var="microsample")

# Merge alpha diversities
alpha_diversity <- richness %>%
      full_join(neutral,by=join_by(microsample==microsample)) %>%
      full_join(phylogenetic,by=join_by(microsample==microsample)) %>%
      left_join(sample_metadata, by=join_by(microsample==microsample))

# Write alpha diversities
alpha_diversity %>% write_tsv("results/alpha_div_unfiltered.tsv")

# Print alpha diversity
alpha_diversity %>%
  select(microsample,richness, neutral, phylogenetic, section, buffer, Xcoord, Ycoord, size) %>%
  tt()
tinytable_srakodzdy7yerla62pth
microsample richness neutral phylogenetic section buffer Xcoord Ycoord size
M300554 252 59.048724 4.005426 Caecum right B11 74953.325 27445.67 4976
M300555 234 29.591689 3.136402 Caecum right B11 72020.280 33695.14 4976
M300556 242 52.377341 3.862228 Caecum right B11 75415.387 27819.35 4976
M300557 252 60.880377 3.919625 Caecum right B11 76113.477 28351.85 4976
M300558 147 16.388623 3.084364 Caecum right B11 NA NA NA
M300559 252 59.602278 4.019172 Caecum right B11 76849.228 29025.05 4976
M300560 252 58.645287 4.181971 Caecum right B11 75971.705 29352.86 4976
M300561 252 57.105278 4.190661 Caecum right B11 76680.937 29558.16 4976
M300562 252 60.378741 4.115130 Caecum right B11 74883.318 29170.18 5140
M300563 252 59.645294 4.072592 Caecum right B11 75220.992 29120.51 5140
M300564 246 52.890970 4.203353 Caecum right B11 75894.617 29134.86 5140
M300565 48 13.113524 4.215440 Caecum right B11 72986.812 36482.20 5140
M300566 251 58.164898 3.882696 Caecum right B11 76922.541 29224.45 5140
M300567 252 57.810869 4.124295 Caecum right B11 77492.203 29097.78 5140
M300568 40 10.638020 2.635867 Caecum right B11 NA NA NA
M300569 252 60.745119 4.196834 Caecum right B11 77495.465 28977.76 5140
M300570 252 57.723816 4.052962 Caecum right B11 74950.841 28473.11 4815
M300571 251 56.661744 4.017740 Caecum right B11 75619.946 28632.40 4815
M300572 249 56.949762 4.191364 Caecum right B11 76345.933 29031.81 4815
M300573 178 34.564442 3.598634 Caecum right B11 74609.411 34469.39 4815
M300574 251 57.725467 4.082745 Caecum right B11 76920.997 29347.99 4815
M300575 135 59.863456 4.655632 Caecum right B11 NA NA NA
M300576 251 57.389815 4.083745 Caecum right B11 77104.532 29588.79 4815
M300577 252 57.842513 4.079376 Caecum right B11 77418.895 29907.92 4815
M300578 252 57.743125 4.012410 Caecum right B12 76897.212 30198.48 5140
M300579 221 38.829262 3.357156 Caecum right B12 73304.285 36352.33 5140
M300580 250 55.871239 4.042301 Caecum right B12 77026.940 30039.53 5140
M300581 252 56.693254 4.077549 Caecum right B12 77028.597 29718.20 5140
M300582 251 55.908533 4.078589 Caecum right B12 77019.213 29448.24 5140
M300583 252 51.029088 4.100996 Caecum right B12 77009.202 28923.10 5140
M300584 252 57.684739 4.058398 Caecum right B12 77019.413 28061.84 5140
M300585 85 36.312174 5.379855 Caecum right B12 NA NA NA
M300586 48 21.091967 4.510739 Caecum right B12 73652.539 35857.69 5141
M300587 8 3.491849 1.592392 Caecum right B12 NA NA NA
M300588 252 54.764773 4.072549 Caecum right B12 75330.017 26890.36 5141
M300589 253 54.565428 4.052600 Caecum right B12 75862.866 27323.96 5141
M300590 252 53.695112 4.232105 Caecum right B12 76508.231 27653.84 5141
M300591 193 44.669792 3.308027 Caecum right B12 76848.926 27815.44 5141
M300592 251 52.703789 4.157326 Caecum right B12 77351.464 28017.27 5141
M300593 253 54.697582 4.159239 Caecum right B12 77854.216 28261.49 5141
M300594 252 57.267685 4.154592 Caecum right B12 75509.650 26477.82 4976
M300595 251 49.303188 4.159722 Caecum right B12 75650.540 26591.91 4976
M300596 252 51.537550 4.129928 Caecum right B12 75822.838 26598.11 4976
M300597 251 52.894386 4.187497 Caecum right B12 76147.102 26625.28 4976
M300598 252 54.366506 4.127848 Caecum right B12 76899.245 26623.52 4976
M300599 252 55.014439 4.041644 Caecum right B12 76852.725 26643.02 4976
M300600 37 12.471508 3.871589 Caecum right B12 NA NA NA
M300601 122 44.752920 6.549661 Caecum right B12 72982.582 21722.53 4976
M300602 195 3.770399 1.526286 Ileum B11 104424.700 42749.48 5140
M300603 172 3.443781 1.761321 Ileum B11 104606.900 42459.54 5140
M300604 54 11.488595 3.430860 Ileum B11 101758.400 36668.70 5140
M300605 154 3.468041 1.580848 Ileum B11 104954.500 42730.89 5140
M300606 231 42.312840 4.055184 Ileum B11 105122.500 42666.74 5140
M300607 25 4.742713 1.877699 Ileum B11 NA NA NA
M300608 180 3.093547 1.514223 Ileum B11 105262.700 42589.77 5140
M300609 207 3.586403 1.515176 Ileum B11 105328.900 42703.60 5140
M300610 193 3.434464 1.521143 Ileum B11 105102.400 41497.10 4976
M300611 75 4.120703 1.781889 Ileum B11 105146.000 41596.22 4976
M300612 186 3.576177 1.512044 Ileum B11 105281.000 41702.52 4976
M300613 71 2.227148 1.360170 Ileum B11 105408.300 41533.66 4976
M300614 51 13.957408 4.473484 Ileum B11 101928.600 37181.60 4976
M300615 76 33.344988 4.963147 Ileum B11 NA NA NA
M300616 174 1.845652 1.249203 Ileum B11 105595.700 41999.37 4976
M300617 236 5.332503 1.984855 Ileum B11 105983.000 42106.21 4976
M300618 56 8.503252 2.626672 Ileum B11 101861.400 37375.71 5306
M300619 175 2.550470 1.410755 Ileum B11 106845.700 41525.80 5306
M300620 28 7.640770 2.905044 Ileum B11 NA NA NA
M300621 119 12.148781 3.349201 Ileum B11 107360.500 41744.06 5306
M300622 221 4.591257 1.766175 Ileum B11 107262.300 42133.87 5306
M300623 160 3.966379 1.799967 Ileum B11 107820.600 41925.02 5306
M300624 115 1.651694 1.232074 Ileum B11 107233.500 41764.35 5306
M300625 144 5.388601 2.320102 Ileum B11 107258.100 42448.02 5306
M300626 41 8.538645 2.863586 Ileum B12 NA NA NA
M300627 144 3.518088 1.512361 Ileum B12 108112.000 45420.81 4815
M300628 175 3.173885 1.607903 Ileum B12 108221.600 45346.45 4815
M300629 182 2.393480 1.450458 Ileum B12 108085.500 45636.13 4815
M300630 182 2.332205 1.406259 Ileum B12 108093.700 45848.93 4815
M300631 208 4.627633 1.966486 Ileum B12 107697.500 45704.29 4815
M300632 139 31.364862 4.012416 Ileum B12 102872.400 38456.93 4815
M300633 216 2.511084 1.495177 Ileum B12 107727.500 45487.09 4815
M300634 213 3.122181 1.540972 Ileum B12 106635.900 42106.55 5384
M300635 30 5.405679 2.215422 Ileum B12 NA NA NA
M300636 204 3.509144 1.743930 Ileum B12 106545.500 42220.70 5384
M300637 51 2.910588 1.509677 Ileum B12 106948.100 42956.50 5384
M300638 203 3.460643 1.642359 Ileum B12 106647.000 42288.86 5384
M300639 224 2.990724 1.567194 Ileum B12 106800.500 41821.88 5384
M300640 139 2.600750 1.476414 Ileum B12 107052.700 42525.49 5384
M300641 98 27.021534 5.575144 Ileum B12 103203.400 38334.96 5384
M300642 72 2.706444 1.584137 Ileum B12 108030.700 43599.50 4976
M300643 16 5.123028 1.769523 Ileum B12 101876.900 39000.58 4976
M300644 225 1.815382 1.244790 Ileum B12 NA NA NA
M300645 192 1.687109 1.278009 Ileum B12 107988.200 43509.47 4976
M300646 64 13.841432 3.496467 Ileum B12 NA NA NA
M300647 201 3.557171 1.509236 Ileum B12 107969.500 43138.84 4976
M300648 198 2.029309 1.315127 Ileum B12 107883.700 43169.50 4976
M300649 74 4.148091 1.828161 Ileum B12 107984.200 43047.52 4976
M300704 248 46.252453 4.111733 Colon B11 10676.967 15665.82 5140
M300705 246 63.904552 3.974667 Colon B11 10812.315 15756.81 5140
M300706 245 55.306851 4.105141 Colon B11 11055.416 15656.04 5140
M300707 249 56.014561 4.107466 Colon B11 11216.842 15649.19 5140
M300708 250 56.919155 3.968289 Colon B11 11879.874 15812.03 5140
M300709 81 47.883513 4.609160 Colon B11 8479.772 19536.22 5140
M300710 51 27.091373 4.608891 Colon B11 NA NA NA
M300711 251 55.676485 4.046441 Colon B11 12278.126 15716.47 5140
M300712 251 58.724925 4.031074 Colon B11 12139.937 15889.85 4976
M300713 21 14.819100 3.257271 Colon B11 8681.188 19729.90 4976
M300714 249 54.478111 4.133304 Colon B11 12138.958 16135.22 4976
M300715 251 57.788457 3.979188 Colon B11 12164.850 16944.14 4976
M300716 249 60.671013 3.921632 Colon B11 12650.442 17948.63 4976
M300717 249 59.400190 4.100718 Colon B11 13434.733 19286.92 4976
M300718 250 59.781144 3.989150 Colon B11 13238.197 20246.16 4976
M300719 64 9.437906 2.619712 Colon B11 NA NA NA
M300720 134 51.228630 4.251175 Colon B11 7385.375 20281.05 5306
M300721 250 62.754999 3.906901 Colon B11 10372.825 20398.48 5306
M300722 247 57.049492 4.044123 Colon B11 11173.110 20408.59 5306
M300724 250 61.740250 4.007957 Colon B11 13295.246 18310.97 5306
M300725 238 59.611724 3.747036 Colon B11 12939.033 18128.54 5306
M300726 89 40.430701 5.493395 Colon B11 NA NA NA
M300727 251 58.839874 4.128478 Colon B11 12777.094 17606.38 5306
M300728 97 56.384971 4.868447 Colon B11 NA NA NA
M300729 236 54.296016 3.909034 Colon B11 12551.788 21653.42 4815
M300730 241 62.293446 4.038759 Colon B11 12478.733 21318.48 4815
M300731 251 60.746384 3.722194 Colon B11 12362.879 20562.75 4815
M300732 227 64.774842 4.057109 Colon B11 12575.296 20313.69 4815
M300733 245 58.847813 3.927334 Colon B11 12653.670 19720.44 4815
M300734 153 57.496349 3.636022 Colon B11 17189.272 29742.58 4815
M300735 251 61.238385 3.925052 Colon B11 11471.313 19136.40 4815
M300736 251 60.609377 3.980455 Colon B11 13507.345 18129.93 5647
M300737 224 64.693351 3.988141 Colon B11 13457.119 17998.50 5647
M300738 247 61.882156 3.928037 Colon B11 13010.058 17942.33 5647
M300739 26 17.627844 4.247952 Colon B11 NA NA NA
M300740 123 55.283007 4.637859 Colon B11 17787.836 12522.88 5647
M300741 250 58.936098 3.954625 Colon B11 12684.368 17716.75 5647
M300742 251 59.273326 4.047533 Colon B11 12621.546 17543.54 5647
M300743 250 60.307163 3.931065 Colon B11 12372.901 16657.60 5647
M300744 245 61.953169 3.854428 Colon B11 11994.451 14153.13 4976
M300745 251 60.978957 3.867243 Colon B11 12007.497 14299.24 4976
M300746 46 10.208392 2.834892 Colon B11 NA NA NA
M300747 250 62.203433 3.804880 Colon B11 12029.348 14662.48 4976
M300748 251 59.304676 3.841718 Colon B11 12076.591 15671.87 4976
M300749 94 51.104739 4.166941 Colon B11 8706.301 29038.15 4976
M300750 251 59.229995 3.963137 Colon B11 12060.510 16688.98 4976
M300751 251 62.453455 3.921567 Colon B11 11931.196 19713.77 4976
M300752 37 10.231365 3.454552 Colon B12 13243.970 30714.35 4815
M300753 250 54.258825 3.870480 Colon B12 13884.299 20066.13 4815
M300754 20 11.105970 3.441836 Colon B12 NA NA NA
M300755 250 56.033041 4.093147 Colon B12 13715.675 19528.97 4815
M300756 250 53.959621 4.076681 Colon B12 13508.645 19087.25 4815
M300757 251 54.271559 4.130368 Colon B12 13209.324 18911.46 4815
M300758 251 60.601778 3.913348 Colon B12 13454.496 18211.88 4815
M300759 252 57.034625 4.139033 Colon B12 13356.627 17525.29 4815
M300760 249 52.510697 4.092732 Colon B12 12866.495 15050.07 5140
M300761 251 55.107864 4.093000 Colon B12 12921.938 15311.99 5140
M300762 28 8.726889 3.118462 Colon B12 NA NA NA
M300763 252 59.548863 4.016797 Colon B12 12995.946 15577.55 5140
M300764 251 58.308107 3.910202 Colon B12 12999.107 16205.10 5140
M300765 177 42.010405 4.149764 Colon B12 13266.800 30315.90 5140
M300766 250 56.763364 4.133256 Colon B12 13128.597 18741.54 5140
M300767 249 51.972455 4.006491 Colon B12 13103.684 20085.08 5140
M300768 249 54.447298 4.031809 Colon B12 12299.778 15261.25 4815
M300769 34 14.270606 3.890768 Colon B12 11581.666 28330.79 4815
M300770 94 30.334103 4.919868 Colon B12 NA NA NA
M300771 248 57.969189 4.027783 Colon B12 12230.636 14216.24 4815
M300772 250 59.731720 3.899035 Colon B12 12192.804 14393.52 4815
M300773 252 62.413288 3.621678 Colon B12 12122.684 16011.33 4815
M300774 251 56.385399 4.122407 Colon B12 12155.624 16716.47 4815
M300775 250 53.553768 4.039717 Colon B12 12941.429 17792.21 4815
M300776 251 57.024440 3.986191 Colon B12 10481.871 16446.70 5306
M300777 215 63.829415 4.004581 Colon B12 10486.437 16559.54 5306
M300778 250 57.359784 4.014746 Colon B12 10349.884 16974.87 5306
M300779 19 10.646900 4.202734 Colon B12 NA NA NA
M300780 251 53.856346 4.031943 Colon B12 10386.112 17635.79 5306
M300781 73 27.241929 4.346054 Colon B12 9381.647 30091.13 5306
M300782 251 53.845025 4.039524 Colon B12 10499.609 18348.85 5306
M300783 251 57.754394 4.054507 Colon B12 10505.179 19231.33 5306
M300784 248 53.052589 4.019137 Colon B12 11637.205 19482.30 4656
M300785 56 41.351511 4.731183 Colon B12 9262.832 30609.58 4656
M300786 249 56.732741 4.172364 Colon B12 11099.177 18995.87 4656
M300787 251 57.074180 4.060990 Colon B12 10460.974 19686.94 4656
M300788 250 54.485767 4.019748 Colon B12 10442.084 20914.36 4656
M300789 56 30.557213 4.776009 Colon B12 NA NA NA
M300790 155 39.641124 3.590062 Colon B12 10801.293 21241.46 4656
M300791 249 49.310887 4.169707 Colon B12 11146.557 21763.22 4656
M300792 251 55.663696 4.257795 Colon B12 11630.334 20543.59 5140
M300793 152 30.393903 3.933883 Colon B12 NA NA NA
M300794 250 56.716658 4.055058 Colon B12 11673.937 21223.36 5140
M300795 208 55.332481 3.811929 Colon B12 11602.686 22068.26 5140
M300796 30 12.304417 4.442865 Colon B12 13661.804 28676.18 5140
M300797 252 51.906800 4.046237 Colon B12 12879.975 20904.88 5140
M300798 251 47.129111 4.133944 Colon B12 12256.492 21371.45 5140
M300799 157 46.746231 3.709551 Colon B12 11843.311 19915.73 5140 
# Print alpha diversity summary
alpha_diversity %>%
  select(richness, neutral, phylogenetic, section, buffer) %>%
  group_by(section, buffer) %>%
  summarise(richness=mean(richness), neutral=mean(neutral), phylogenetic=mean(phylogenetic)) %>%
  tt()
tinytable_5i3be4cibzi0xfjsaeul
section buffer richness neutral phylogenetic
Caecum right B11 220.6250 50.239502 3.942011
Caecum right B12 208.0833 46.973329 4.100613
Colon B11 204.8085 53.573038 4.004198
Colon B12 198.3750 46.906424 4.037582
Ileum B11 137.4167 7.924440 2.229897
Ileum B12 145.4583 6.016212 1.983800 
alpha_diversity %>%
  pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
  left_join(quality,by=join_by(microsample==microsample)) %>%
  mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
  ggplot(aes(x=section, y=value, color=quality, group=section))+ 
        scale_color_gradient(low = "red", high = "green", name = "Quality") +
        geom_boxplot(outlier.shape = NA) +
        geom_jitter(width=0.2) + 
        facet_grid(metric ~ section, scales = "free")